[2023-03-18 22:23:56,363] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:23:56,363] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:23:56,364] [INFO] DQC Reference Directory: /var/lib/cwl/stge477fa88-bfb6-4deb-943f-0b9d46bb1906/dqc_reference
[2023-03-18 22:23:57,543] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:23:57,544] [INFO] Task started: Prodigal
[2023-03-18 22:23:57,544] [INFO] Running command: cat /var/lib/cwl/stg861524ff-274a-4392-912f-3c275c987667/OceanDNA-b10418.fa | prodigal -d OceanDNA-b10418/cds.fna -a OceanDNA-b10418/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:24:05,801] [INFO] Task succeeded: Prodigal
[2023-03-18 22:24:05,801] [INFO] Task started: HMMsearch
[2023-03-18 22:24:05,801] [INFO] Running command: hmmsearch --tblout OceanDNA-b10418/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge477fa88-bfb6-4deb-943f-0b9d46bb1906/dqc_reference/reference_markers.hmm OceanDNA-b10418/protein.faa > /dev/null
[2023-03-18 22:24:05,985] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:24:05,986] [INFO] Found 6/6 markers.
[2023-03-18 22:24:05,996] [INFO] Query marker FASTA was written to OceanDNA-b10418/markers.fasta
[2023-03-18 22:24:05,997] [INFO] Task started: Blastn
[2023-03-18 22:24:05,997] [INFO] Running command: blastn -query OceanDNA-b10418/markers.fasta -db /var/lib/cwl/stge477fa88-bfb6-4deb-943f-0b9d46bb1906/dqc_reference/reference_markers.fasta -out OceanDNA-b10418/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:24:06,580] [INFO] Task succeeded: Blastn
[2023-03-18 22:24:06,582] [INFO] Selected 23 target genomes.
[2023-03-18 22:24:06,582] [INFO] Target genome list was writen to OceanDNA-b10418/target_genomes.txt
[2023-03-18 22:24:06,594] [INFO] Task started: fastANI
[2023-03-18 22:24:06,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg861524ff-274a-4392-912f-3c275c987667/OceanDNA-b10418.fa --refList OceanDNA-b10418/target_genomes.txt --output OceanDNA-b10418/fastani_result.tsv --threads 1
[2023-03-18 22:24:19,278] [INFO] Task succeeded: fastANI
[2023-03-18 22:24:19,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge477fa88-bfb6-4deb-943f-0b9d46bb1906/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:24:19,279] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge477fa88-bfb6-4deb-943f-0b9d46bb1906/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:24:19,282] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:24:19,282] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:24:19,282] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	75.0978	60	478	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:24:19,282] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10418/tc_result.tsv
[2023-03-18 22:24:19,282] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:24:19,282] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:24:19,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge477fa88-bfb6-4deb-943f-0b9d46bb1906/dqc_reference/checkm_data
[2023-03-18 22:24:19,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:24:19,394] [INFO] Task started: CheckM
[2023-03-18 22:24:19,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10418/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10418/checkm_input OceanDNA-b10418/checkm_result
[2023-03-18 22:24:44,840] [INFO] Task succeeded: CheckM
[2023-03-18 22:24:44,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:24:44,843] [INFO] ===== Completeness check finished =====
[2023-03-18 22:24:44,843] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:24:44,844] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10418/markers.fasta)
[2023-03-18 22:24:44,844] [INFO] Task started: Blastn
[2023-03-18 22:24:44,845] [INFO] Running command: blastn -query OceanDNA-b10418/markers.fasta -db /var/lib/cwl/stge477fa88-bfb6-4deb-943f-0b9d46bb1906/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10418/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:24:45,790] [INFO] Task succeeded: Blastn
[2023-03-18 22:24:45,791] [INFO] Selected 21 target genomes.
[2023-03-18 22:24:45,791] [INFO] Target genome list was writen to OceanDNA-b10418/target_genomes_gtdb.txt
[2023-03-18 22:24:45,802] [INFO] Task started: fastANI
[2023-03-18 22:24:45,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg861524ff-274a-4392-912f-3c275c987667/OceanDNA-b10418.fa --refList OceanDNA-b10418/target_genomes_gtdb.txt --output OceanDNA-b10418/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:24:52,428] [INFO] Task succeeded: fastANI
[2023-03-18 22:24:52,433] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:24:52,433] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002169155.2	s__TMED220 sp002169155	96.464	221	478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED220	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905381055.1	s__TMED220 sp905381055	87.4958	431	478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED220	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702875.1	s__TMED220 sp002702875	76.3267	105	478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED220	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690805.1	s__GCA-002723295 sp002690805	76.0672	59	478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	97.07	97.07	0.76	0.76	2	-
GCA_905182735.1	s__GCA-002723295 sp905182735	75.9636	63	478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560065.1	s__GCA-2719315 sp902560065	75.9624	61	478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2719315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719315.1	s__GCA-2719315 sp002719315	75.8883	91	478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2719315	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:24:52,434] [INFO] GTDB search result was written to OceanDNA-b10418/result_gtdb.tsv
[2023-03-18 22:24:52,434] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:24:52,435] [INFO] DFAST_QC result json was written to OceanDNA-b10418/dqc_result.json
[2023-03-18 22:24:52,435] [INFO] DFAST_QC completed!
[2023-03-18 22:24:52,435] [INFO] Total running time: 0h0m56s